Mercurial > repos > imgteam > anisotropic_diffusion
comparison anisotropic_diffusion.py @ 0:d13e26f576bc draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:30:00 -0500 |
| parents | |
| children | 17d3cfba9b5a |
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| -1:000000000000 | 0:d13e26f576bc |
|---|---|
| 1 import argparse | |
| 2 import sys | |
| 3 import warnings | |
| 4 import numpy as np | |
| 5 import skimage.io | |
| 6 import skimage.util | |
| 7 from medpy.filter.smoothing import anisotropic_diffusion | |
| 8 | |
| 9 parser = argparse.ArgumentParser() | |
| 10 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | |
| 11 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | |
| 12 parser.add_argument('niter', type=int, help='Number of iterations', default=1) | |
| 13 parser.add_argument('kappa', type=int, help='Conduction coefficient', default=50) | |
| 14 parser.add_argument('gamma', type=float, help='Speed of diffusion', default=0.1) | |
| 15 parser.add_argument('eqoption', type=int, choices=[1,2], help='Perona Malik diffusion equation', default=1) | |
| 16 args = parser.parse_args() | |
| 17 | |
| 18 with warnings.catch_warnings(): | |
| 19 warnings.simplefilter("ignore") #to ignore FutureWarning as well | |
| 20 | |
| 21 img_in = skimage.io.imread(args.input_file.name, plugin='tifffile') | |
| 22 res = anisotropic_diffusion(img_in, niter=args.niter, kappa=args.kappa, gamma=args.gamma, option=args.eqoption) | |
| 23 res[res<-1]=-1 | |
| 24 res[res>1]=1 | |
| 25 | |
| 26 res = skimage.util.img_as_uint(res) #Attention: precision loss | |
| 27 | |
| 28 skimage.io.imsave(args.out_file.name, res, plugin='tifffile') |